DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of the species colon cancer in the reply filed on February 17th, 2026 is acknowledged.
After further consideration, the species election is hereby withdrawn. All cancers claimed in claim 24 will be considered.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 18th, 2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Summary
Claim 9 has been amended. Claims 4, 6-7, 17, 19, 25-30, and 32 have been canceled. Claims 1-3, 5, 8-16, 18, 20-24, and 31 are pending. Claims 1-3, 5, 8-16, 18, 20-24, and 31 are under examination and discussed in this Office action.
Specification
The use of the terms such as Apple, Samsung, and SYBR, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5 and 13 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 5 recites the limitation “subsequent to (b) subjecting a nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, to nucleic acid amplification to generate a plurality of amplification products, wherein (b) comprises subjecting said plurality of amplification products or derivatives thereof to sequencing to generate a plurality of sequence reads”. It is unclear from this recitation how the amplification could happen subsequent to step (b) when step (b) then comprises subjecting the amplification products to sequencing. The language “subsequent to” indicates that the amplification is happening after step (b). If this is the case, it would not be possible for the amplification products to be sequenced in step (b) as claimed. It is also unclear from this recitation whether the recitation of “or a derivative thereof” following “said second plurality of nucleic acid molecules” is intended to be an option only for the second plurality of nucleic acid molecules, or if there is intended to be an option to use derivatives of the first plurality of nucleic acid molecules as well. Therefore, the claim is found indefinite.
Claim 13 recites the limitation “wherein (c) further comprises processing said plurality of sequence reads to determine a size for at least a subset of said first or second plurality of nucleic acid molecules”. It is unclear from this recitation what determining a size for at least a subset of said second plurality of nucleic acid molecules entails given that it is known from claim 1 that the second plurality of nucleic acid molecules have a predetermined size. Presumably, based on the claim language presented in claim 1, the size of the second plurality of nucleic acids is already known and would not need to be determined again from the plurality of sequence reads. Therefore, the claim is found indefinite.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 5, 8-16, 18, 20-24, and 31 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas and a natural phenomenon without significantly more. While the claims are directed to a process, and therefore meet step 1 of the subject matter eligibility test (see MPEP 2106.03), the claim(s) recite the abstract ideas of processing a plurality of sequence reads to identify reads corresponding to the first plurality of nucleic acid molecules and the second plurality of nucleic acid molecules, as well as using the second set of sequence reads to identify molecules from the first plurality of nucleic acid molecules that have a predetermined size. These are considered abstract ideas because they can be considered mental processes, and can reasonably be performed in the human mind. The claims also recite the natural correlation between a change in a sample nucleic acid sequence and determining having or a risk of having a disease. Such correlation is a natural phenomenon because it describes a consequence of natural processes in the human body.
Step 2A of the subject matter eligibility test requires a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP 2106.04(II)(A)(1), the meaning of “recites” is “set forth” or “describes”. That is, a claim recites a judicial exception when the judicial exception is “set forth” or “described” in the claim. In the instant case, the claims describe a natural phenomenon: the abstract ideas of processing a plurality of sequence reads to identify reads corresponding to the first plurality of nucleic acid molecules and the second plurality of nucleic acid molecules, as well as using the second set of sequence reads to identify molecules from the first plurality of nucleic acid molecules that have a predetermined size; and the natural phenomenon of a change in a sample nucleic acid sequence and determining having or a risk of having a disease.
Prong Two of the analysis under step 2A asks: does the claim recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP 2106.04(II)(A)(2), “Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.” The considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP 2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or other technology. While the instant claims recite steps of (a) generating a mixture comprising (i) a first plurality of nucleic acid molecules derived from a biological sample of a subject, and (ii) a second plurality of nucleic acid molecules comprising sequences having at least one predetermined size; (b) subjecting said (i) first plurality of nucleic acid molecules, or derivative thereof; and (ii) second plurality of nucleic acid molecules or derivative thereof, to sequencing to generate a plurality of sequence reads; and (c) processing said plurality of sequence reads to identify (i) a first set of sequence reads corresponding to at least a subset of said first plurality of nucleic acid molecules, and (ii) a second set of sequence reads corresponding to at least a subset of said second plurality of nucleic acid molecules, which second set of sequence reads corresponds to said sequences having said at least one predetermined size; and (d) using said second set of sequence reads to identify one or more nucleic acid molecules of said first plurality of nucleic acid molecules as having said at least one predetermined size; subsequent to (a) using said first plurality of nucleic acid molecules and said second plurality of nucleic acid molecules to generate a third plurality of nucleic acid molecules; wherein generating said third plurality of nucleic acid molecules comprises (a) ligating ends of a nucleic acid molecule of said first or second plurality of nucleic acid molecules, or a derivative thereof, to one another or (b) coupling an adapter to a 3' end, a 5' end or both a 5' end and a 3' end of a nucleic acid molecule of said first or second plurality of nucleic acid molecules, or a derivative thereof; subsequent to (b) subjecting a nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, to nucleic acid amplification to generate a plurality of amplification products, wherein (b) comprises subjecting said plurality of amplification products or derivatives thereof to sequencing to generate a plurality of sequence reads; wherein said nucleic acid amplification comprises contacting said nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, to an amplification reaction mixture comprising random primers; wherein said nucleic acid amplification comprises contacting said nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, or a derivative thereof, to an amplification reaction mixture comprising one or more primers, each of which specifically hybridizes to a different target sequence via sequence complementarity; wherein said second plurality of nucleic acid molecules comprises (i) a 5' common sequence, (ii) a 3' common sequence, or (iii) a 5' common sequence and a 3' common sequence; wherein said second plurality of nucleic acid molecules comprises a fixed molar ratio of nucleic acid molecules of each predetermined size; using said second set of sequence reads to normalize a molar ratio of said first plurality of nucleic acid molecules of each predetermined size; wherein (c) further comprises processing said plurality of sequence reads to determine a size for at least a subset of said first or second plurality of nucleic acid molecules; wherein said first or second plurality of nucleic acid molecules is single stranded; wherein said first plurality of nucleic acid molecules of said biological sample comprises cell-free deoxyribonucleic acid (DNA) or cell-free ribonucleic acid (RNA); wherein said first plurality of nucleic acid molecules of said biological sample is from a tumor; wherein said biological sample comprises a bodily fluid selected from urine, saliva, blood, serum, plasma, tears, sputum, cerebrospinal fluid, synovial fluid, mucus, bile, semen, lymph, amniotic fluid, menstrual fluid, or combinations thereof; wherein said biological sample is a cell-free biological sample; subsequent to (d) using said second set of sequence reads to normalize said one or more nucleic acid molecules of said first plurality of nucleic acid molecules having said at least one predetermined size; processing said first set of sequence reads with a reference set of sequence reads to identify a change in said first set of sequence reads thereby determining that a subject has or is at risk of having a disease; wherein said disease is cancer; wherein said cancer is selected from the group consisting of colon cancer, non-small cell lung cancer, small cell lung cancer, breast cancer, hepatocellular carcinoma, liver cancer, skin cancer, malignant melanoma, endometrial cancer, esophageal cancer, gastric cancer, ovarian cancer, pancreatic cancer, brain cancer, leukemia, lymphoma, and myeloma; and wherein said second plurality of nucleic acid molecules comprises sequences having at least two predetermined sizes, the claims do not improve upon sequencing techniques, amplification techniques, or sequencing analysis. The claims merely use existing methods for these steps. Note that MPEP 2106.05(a) indicates that “[u]sing well-known standard laboratory techniques to detect enzyme levels in a bodily sample” is an example that the courts have indicated may not be sufficient to show an improvement to technology.
MPEP 2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine. While the instant claims recite steps as detailed above, no such machines are required by the claim, and certainly no particular machines. Even if some conventional machine were recited in the claims, like a specific sequencing device or amplification device, further considerations such as the particularity or generality of the recited machine must be taken into account, as well as whether the involvement of the machine is merely extra-solution activity. MPEP 2106.05(g) describes “extra-solution activity”, noting that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra-solution activity.
MPEP 2106.05(c) has to do with whether the claims involve a particular transformation. Here, none of the limitations of the claims involve a particular transformation. For example, sequencing nucleic acid molecules does not transform those molecules into something else during the sequencing process.
MPEP 2106.05(e) has to do with “other meaningful limitations”. The additional limitations imposed upon the abstract ideas of processing a plurality of sequence reads to identify reads corresponding to the first plurality of nucleic acid molecules and the second plurality of nucleic acid molecules, as well as using the second set of sequence reads to identify molecules from the first plurality of nucleic acid molecules that have a predetermined size; and the natural phenomenon of a change in a sample nucleic acid sequence and determining having or a risk of having a disease in the instant case have to do with generating a sample mixture, sequencing, generating a third plurality of nucleic acid molecules, ligation, amplification, common sequences in the second plurality of nucleic acid molecules, determining fixed molar ratios, determining sequence read sizes, nucleic acid molecules being single stranded, nucleic acid molecules being cfDNA or cfRNA, the sample coming from a tumor, other sample types, normalization, types of cancer, and the second plurality of nucleic acid molecules having at least 2 pre-determined sizes. These limitations are not considered “meaningful limitations”. MPEP 2106.05(e) states: “The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements that provide an inventive concept to the claim as a whole.” However, as will be discussed below, these limitations do not arrive at an inventive concept. In addition, as has been discussed, they represent insignificant extra-solution activity, i.e. “data gathering”.
MPEP 2106.05(f) raises the question as to whether the additional elements recited in the claim represent “mere instructions to apply an exception”. Here, the judicial exceptions are the abstract ideas of processing a plurality of sequence reads to identify reads corresponding to the first plurality of nucleic acid molecules and the second plurality of nucleic acid molecules, as well as using the second set of sequence reads to identify molecules from the first plurality of nucleic acid molecules that have a predetermined size; and the natural phenomenon of a change in a sample nucleic acid sequence and determining having or a risk of having a disease. The additional elements recited in the claims (i.e. generating a sample mixture, sequencing, generating a different plurality of nucleic acid molecules, ligation, amplification, common sequences in the second plurality of nucleic acid molecules, determining fixed molar ratios, determining sequence read sizes, nucleic acid molecules being single stranded, nucleic acid molecules being cfDNA or cfRNA, the sample coming from a tumor, other sample types, normalization, types of cancer, and the second plurality of nucleic acid molecules having at least 2 pre-determined sizes) do amount to mere instructions to apply the judicial exceptions, since the these steps serve as mere conventional steps taken for the purpose of gathering data that is processed during the abstract ideas, and also gathering data to determine having or a risk of having a disease, which any practical use of the judicial exceptions would require.
MPEP 2106.05(g) has to do with whether the additional elements of the claim amount to insignificant extra-solution activity. MPEP 2106.05(g) notes that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra - solution activity. Likewise, MPEP 2106.05(g) notes that “[p]erforming clinical tests on individuals to obtain input for an equation” also represents insignificant extra-solution activity. This aligns closely with the instant claims, where the additional elements of the claims amount to generating a sample mixture, sequencing, generating a different plurality of nucleic acid molecules, ligation, amplification, common sequences in the second plurality of nucleic acid molecules, determining fixed molar ratios, determining sequence read sizes, nucleic acid molecules being single stranded, nucleic acid molecules being cfDNA or cfRNA, the sample coming from a tumor, other sample types, normalization, types of cancer, and the second plurality of nucleic acid molecules having at least 2 pre-determined sizes.
MPEP 2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. Here, the recitation of the method being used for nucleic acid processing or analysis is considered a “field of use”. However, as MPEP 2106.05(h) indications, such limiting to a particular “field of use” does not confer patentability on otherwise ineligible subject matter.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions (as set forth in step 2B of the subject matter eligibility test; see MPEP 2106-III) because it was routine and conventional in the prior art to use control nucleic acids as an add-in comparison tool against sample nucleic acids to evaluate sequencing.
For example, Mortimer (US 20200232010 A1) teaches (a) generating a mixture comprising (i) a first plurality of nucleic acid molecules derived from a biological sample of a subject, and (ii) a second plurality of nucleic acid molecules comprising sequences having at least one predetermined size (Page 1, paragraph [0004]); (b) subjecting said (i) first plurality of nucleic acid molecules, or derivative thereof; and (ii) second plurality of nucleic acid molecules or derivative thereof, to sequencing to generate a plurality of sequence reads (Page 1, paragraph [0004]); subsequent to (a) using said first plurality of nucleic acid molecules and said second plurality of nucleic acid molecules to generate a third plurality of nucleic acid molecules (Page 1, paragraph [0004]); wherein generating said third plurality of nucleic acid molecules comprises (a) ligating ends of a nucleic acid molecule of said first or second plurality of nucleic acid molecules, or a derivative thereof, to one another or (b) coupling an adapter to a 3' end, a 5' end or both a 5' end and a 3' end of a nucleic acid molecule of said first or second plurality of nucleic acid molecules, or a derivative thereof (Page 1, paragraph [0004]); subsequent to (b) subjecting a nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, to nucleic acid amplification to generate a plurality of amplification products, wherein (b) comprises subjecting said plurality of amplification products or derivatives thereof to sequencing to generate a plurality of sequence reads (Page 1, paragraph [0004]); wherein said nucleic acid amplification comprises contacting said nucleic acid molecule of said first plurality of nucleic acid molecules or said second plurality of nucleic acid molecules, or a derivative thereof, to an amplification reaction mixture comprising primers (Pages 27-28, paragraph [0227]); wherein said second plurality of nucleic acid molecules comprises (i) a 5' common sequence, (ii) a 3' common sequence, or (iii) a 5' common sequence and a 3' common sequence (Page 1, paragraph [0006]); wherein said second plurality of nucleic acid molecules comprises a fixed molar ratio of nucleic acid molecules of each predetermined size (Pages 1-2, paragraph [0014]); using said second set of sequence reads to normalize a molar ratio of said first plurality of nucleic acid molecules of each predetermined size (Page 14, paragraph [0138]); wherein (c) further comprises processing said plurality of sequence reads to determine a size for at least a subset of said first or second plurality of nucleic acid molecules (Pages 16-17, paragraph [0154]); wherein said first or second plurality of nucleic acid molecules is single stranded (Page 9, paragraph [0098]); wherein said first plurality of nucleic acid molecules of said biological sample comprises cell-free deoxyribonucleic acid (DNA) or cell-free ribonucleic acid (RNA) (Page 1, paragraph [0004]); wherein said first plurality of nucleic acid molecules of said biological sample is from a tumor (Pages 25-26, paragraph [0210]); wherein said biological sample comprises a bodily fluid selected from urine, saliva, blood, serum, plasma, tears, sputum, cerebrospinal fluid, synovial fluid, mucus, bile, semen, lymph, amniotic fluid, menstrual fluid, or combinations thereof (Pages 25-26, paragraph [0210]); wherein said biological sample is a cell-free biological sample (Pages 25-26, paragraph [0210]); subsequent to (d) using said second set of sequence reads to normalize said one or more nucleic acid molecules of said first plurality of nucleic acid molecules having said at least one predetermined size (Page 14, paragraph [0138]); processing said first set of sequence reads with a reference set of sequence reads to identify a change in said first set of sequence reads thereby determining that a subject has or is at risk of having a disease (Page 29, paragraph [0244]); wherein said disease is cancer (Pages 32-33, paragraph [0273]); wherein said cancer is selected from the group consisting of colon cancer, non-small cell lung cancer, small cell lung cancer, breast cancer, hepatocellular carcinoma, liver cancer, skin cancer, malignant melanoma, endometrial cancer, esophageal cancer, gastric cancer, ovarian cancer, pancreatic cancer, brain cancer, leukemia, lymphoma, and myeloma (Pages 32-33, paragraph [0273]); and wherein said second plurality of nucleic acid molecules comprises sequences having at least two predetermined sizes (Page 1, paragraph [0009]).
Having considered the factors discussed in MPEP 2106.04(c)(II) and MPEP 2106.05 (a)-(c) and (e)-(h), as well as the prior art of Mortimer, it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exceptions into a practical application of those exceptions in such a way as to provide meaningful limits on the use of the judicial exceptions. Therefore, claims 1-3, 5, 8-16, 18, 20-24, and 31 are rejected here under 35 U.S.C. 101.
Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Mortimer (US 20200232010 A1) teaches on fragment size control molecules with a pre-determined size as spike-in additions to samples of cell-free polynucleotides (Page 1, paragraphs [0004] and [0006]). These control molecules are sequenced along with the sample (Page 1, paragraph [0004]). Mortimer teaches sample and control molecules are amplified prior to sequencing (Page 1, paragraph [0004]). Mortimer teaches that subsets of fragment control molecules are present in equimolar concentrations (Pages 1-2, paragraph [0014]). Mortimer teaches normalizing the sample molecules using the fragment size control molecules (Page 14, paragraph [0138]). Mortimer teaches biological samples comprising a tumor; a bodily fluid selected from urine, saliva, blood, serum, plasma, tears, sputum, cerebrospinal fluid, synovial fluid, mucus, bile, semen, lymph, amniotic fluid, menstrual fluid, or combinations thereof; and a cell-free biological sample (Pages 25-26, paragraph [0210]). Mortimer teaches aligning reads to a reference genome to aid diagnosis of disease (Page 29, paragraph [0244]), wherein said disease is cancer (Pages 32-33, paragraph [0273]). However, Mortimer does not teach step (d) of claim 1, wherein a second plurality of sequence reads with at least one predetermined size are used to identify one or more nucleic acid molecules from a first plurality as having said at least one predetermined size.
Lin (US 20190323073 A1; cited on the IDS filed July 18th, 2023) teaches on cell-free nucleic acid standards with a size range of 100-300 bases as spike-in additions to samples of cell-free nucleic acids to calibrate abundance of sample cell-free nucleic acids (Page 1, paragraph [0006]). These control molecules are sequenced along with the sample (Page 2, paragraph [0013]). Lin teaches sample and control molecules are amplified prior to sequencing (Page 2, paragraphs [0012]-[0013]). Lin teaches that abundance can be determined using molar concentration (Page 7, paragraph [0059]). Lin teaches normalizing the sample cell-free nucleic acids using the cell-free nucleic acid standards (Page 9, paragraph [0071]). Lin teaches biological samples comprising a tumor; a bodily fluid selected from urine, saliva, blood, serum, plasma, tears, sputum, cerebrospinal fluid, synovial fluid, mucus, bile, semen, lymph, amniotic fluid, menstrual fluid, or combinations thereof; and a cell-free biological sample (Page 20, paragraph [0144]; Page 21, paragraph [0149]). Lin teaches deriving cell-free nucleic acid samples from diseased cells, such as cancer cells (Page 20, paragraph [0144]). However, Lin does not teach step (d) of claim 1, wherein a second plurality of sequence reads with at least one predetermined size are used to identify one or more nucleic acid molecules from a first plurality as having said at least one predetermined size.
Conclusion
All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Allison E Schloop whose telephone number is (703)756-4597. The examiner can normally be reached Monday-Friday 8:30-5 ET.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
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